pyproject.toml

[project]
name = "biolab"
version = "0.1.0"
description = "BioLab — unified bioinformatics platform for gene analysis, evidence synthesis, and whole-cell simulation"
requires-python = ">=3.11"
dependencies = [
    "fastapi>=0.115",
    "uvicorn[standard]>=0.34",
    "httpx>=0.28",
    "pydantic>=2.10",
    "pydantic-settings>=2.3",
    "biopython>=1.84",
    "websockets>=14.0",
    "asyncio-throttle>=1.0",
    "pyyaml>=6.0",
    "sqlalchemy>=2.0",
    "alembic>=1.13",
    "typer[all]>=0.12",
    "rich>=13.7",
    "python-multipart>=0.0.9",
    "numpy>=1.24",
    "scipy>=1.11",
]

[project.optional-dependencies]
postgres = ["psycopg2-binary>=2.9"]
pipelines = ["dagster>=1.7", "dagster-webserver>=1.7"]
llm = ["openai>=1.0"]
ml = ["torch>=2.0", "transformers>=4.30"]
validation = ["libroadrunner>=2.4", "matplotlib>=3.7", "pandas>=2.0"]
dashboard = [
    "streamlit>=1.30",
    "pycirclize>=1.0",
    "plotly>=5.0",
    "streamlit-molstar>=0.8",
]
cellforge = [
    "cobra>=0.29",
    "gillespy2>=1.8",
    "redis>=5.0",
    "pyarrow>=14.0",
    "zarr>=2.16",
    "h5py>=3.10",
    "equilibrator-api>=0.4",
]
dev = [
    "pytest>=8.0",
    "pytest-asyncio>=0.24",
    "pytest-cov>=5.0",
    "ruff>=0.8",
    "mypy>=1.8",
]

[project.scripts]
biolab = "biolab.cli.main:app"

[build-system]
requires = ["maturin>=1.7"]
build-backend = "maturin"

[tool.maturin]
python-source = "src"
module-name = "biolab.cellforge._engine"
manifest-path = "crates/cellforge-engine/Cargo.toml"

[tool.pytest.ini_options]
testpaths = ["tests"]
asyncio_mode = "auto"

[tool.dagster]
module_name = "biolab.pipelines.definitions"

[tool.ruff]
line-length = 100
target-version = "py311"
src = ["src"]

[tool.ruff.lint]
select = ["E", "F", "I", "UP", "B", "SIM"]

[tool.mypy]
python_version = "3.11"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true